Synced with new Mac, lost a whole bunch of songs and apps

My computers:
- A Mac Pro tower running OS 10.6.8 and iTunes 10.5.2 (11).
- A vanilla MacBook also running OS 10.6.8. and iTunes 10.5.2 (11).

My device:
- An iPhone 3GS running iOS 5.

I always synced the phone to my Mac Pro. Today I plugged it into my MacBook to charge it. Sometimes when I do this, iTunes opens automatically, and I close it to avoid syncing. Today I got a message I never saw before, one I assume is part of the newest iTunes: it said (and sorry I can't get the exact message) something to the effect of needing to authorize this computer.

I Google this and learn that apparently, I can authorize up to 5 devices, and stuff will sync when I plug my phone to any of those devices. So I go ahead with this and let the sync happen.

After the sync, I lost a lot of music and apps. Not everything, but there's no rhyme and reason to what I did lose. As an example: I lost the Bastion soundtrack, which I purchased from Supergiant and transferred to iTunes. I also lost the Podcaster app which I got from the App Store. And the Blizzard Authenticator. But again, not everything; some apps and music remained.

However, now I'm nervous. My Mac Pro should still have all the apps and songs I lost, but what happens when I plug my phone back into it? Will I suddenly lose everything there too?

Any help would be super-appreciated, as this issue has left this Apple supporter rather jaded and nervous.